KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing

Caleb M Dillingham; Harshini Cormaty; Ellen C Morgan; Andrew I Tak; Dakarai E Esgdaille; Paul L Boutz; Rupa Sridharan

doi:10.1101/2023.05.31.543088

KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing

bioRxiv [Preprint]. 2024 Jan 23:2023.05.31.543088. doi: 10.1101/2023.05.31.543088.

Authors

Caleb M Dillingham^{1

2

3}, Harshini Cormaty^{1

2

4}, Ellen C Morgan^{1

2}, Andrew I Tak^{1

2

5}, Dakarai E Esgdaille⁶, Paul L Boutz⁷, Rupa Sridharan^{1

2}

Affiliations

¹ Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.
² Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA.
³ Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
⁴ Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
⁵ Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA.
⁶ Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry.
⁷ Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry.

Abstract

Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cell (ESC) identity is characterized by a lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 family of histone demethylases removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. Acute selective degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.

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